scholarly journals Applications of the Local Mode Model to CH Bond Length Changes, Molecular Conformations and Vibrational Dynamics

1983 ◽  
Vol 2 (5-6) ◽  
pp. 309-320 ◽  
Author(s):  
Bryan R. Henry ◽  
Kathleen M. Gough
Keyword(s):  
Bond Length ◽  
Gas Phase ◽  
Theoretical Basis ◽  
Local Mode ◽  
Vibrational Dynamics ◽  
Molecular Conformations ◽  
Aromatic Molecules ◽  
Length Changes

The theoretical basis for the local mode model is reviewed. The model is applied to gas phase overtone spectra of aromatic molecules to investigate both substituent induced CH bond length changes and conformationally inequivalent hydrogens. The dynamic implications of the local mode model are discussed.

An origin of excess vibrational entropies at grain boundaries in Al, Si and MgO: a first-principles analysis with lattice dynamics

2021 ◽  
Author(s):  
T. Yokoi ◽  
K. Ikawa ◽  
A. Nakamura ◽  
K. Matsunaga
Keyword(s):  
Bond Length ◽  
Grain Boundaries ◽  
First Principles ◽  
Lattice Dynamics ◽  
Excess Entropy ◽  
First Principle ◽  
Length Changes

Excess vibrational entropies are examined by performing first-principle lattice dynamics for grain boundaries in MgO, Al and Si. Bond-length changes are critical for excess entropy, although their bonding nature is originally very different.

Redshift or Adduct Stabilization—A Computational Study of Hydrogen Bonding in Adducts of Protonated Carboxylic Acids

2009 ◽  
Vol 15 (2) ◽  
pp. 239-248 ◽  
Author(s):  
Solveig Gaarn Olesen ◽  
Steen Hammerum
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Bond Strength ◽  
Bond Length ◽  
Carboxylic Acids ◽  
Computational Study ◽  
Proton Affinities ◽  
Oh Groups ◽  
Hydrogen Bond Strength ◽  
Length Changes

It is generally expected that the hydrogen bond strength in a D–H•••A adduct is predicted by the difference between the proton affinities (Δ PA) of D and A, measured by the adduct stabilization, and demonstrated by the infrared (IR) redshift of the D–H bond stretching vibrational frequency. These criteria do not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The Δ PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength.

Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

2010 ◽  
Vol 66 (5) ◽  
pp. 527-543 ◽  
Author(s):  
Leonardo Lo Presti ◽  
Raffaella Soave ◽  
Mariangela Longhi ◽  
Emanuele Ortoleva
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Phase Ii ◽  
Density Functional ◽  
Organic Ligand ◽  
Stable Phase ◽  
Stable Form ◽  
Molecular Conformations

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.111,15.02,6.016,20)triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C24H30N6) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z′, density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z′ = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30–40 kJ mol−1. These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

scholarly journals An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3323 ◽  
Author(s):  
Sahar Nikoo ◽  
Paul Meister ◽  
John Hayward ◽  
James Gauld
Keyword(s):  
Inorganic Chemistry ◽  
Bond Length ◽  
Gas Phase ◽  
Electron Correlation ◽  
Negative Charge ◽  
Basis Set ◽  
Proton Affinities ◽  
Selenium Compounds ◽  
Gas Phase Basicities

The heavier chalcogens sulfur and selenium are important in organic and inorganic chemistry, and the role of such chalcogens in biological systems has recently gained more attention. Sulfur and, to a lesser extent selenium, are involved in diverse reactions from redox signaling to antioxidant activity and are considered essential nutrients. We investigated the ability of the DFT functionals (B3LYP, B3PW91, ωB97XD, M06-2X, and M08-HX) relative to electron correlation methods MP2 and QCISD to produce reliable and accurate structures as well as thermochemical data for sulfur/selenium-containing systems. Bond lengths, proton affinities (PA), gas phase basicities (GPB), chalcogen–chalcogen bond dissociation enthalpies (BDE), and the hydrogen affinities (HA) of thiyl/selenyl radicals were evaluated for a range of small polysulfur/selenium compounds and cysteine per/polysulfide. The S–S bond length was found to be the most sensitive to basis set choice, while the geometry of selenium-containing compounds was less sensitive to basis set. In mixed chalcogens species of sulfur and selenium, the location of the sulfur atom affects the S–Se bond length as it can hold more negative charge. PA, GPB, BDE, and HA of selenium systems were all lower, indicating more acidity and more stability of radicals. Extending the sulfur chain in cysteine results in a decrease of BDE and HA, but these plateau at a certain point (199 kJ mol−1 and 295 kJ mol−1), and PA and GPB are also decreased relative to the thiol, indicating that the polysulfur species exist as thiolates in a biological system. In general, it was found that ωB97XD/6-311G(2d,p) gave the most reasonable structures and thermochemistry relative to benchmark calculations. However, nuances in performance are observed and discussed.

ChemInform Abstract: BOND LENGTH CHANGES RESULTING FROM HALOGEN SUBSTITUTION OF OXIRANE

1985 ◽  
Vol 16 (11) ◽  
Author(s):  
C. A. DEAKYNE ◽  
J. P. CRAVERO ◽  
W. S. HOBSON
Keyword(s):  
Bond Length ◽  
Length Changes
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